HEADER MEMBRANE PROTEIN 18-DEC-20 7BC7 TITLE CRYO-EM STRUCTURE OF THE PROTON COUPLED FOLATE TRANSPORTER AT PH 6.0 TITLE 2 BOUND TO PEMETREXED COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTON-COUPLED FOLATE TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NANOBODY; COMPND 7 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: PCFT; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 10 ORGANISM_TAXID: 9844 KEYWDS TRANSPORTER FOLATE PROTON SYMPORTER, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.L.PARKER,J.C.DEME,S.M.LEA,S.NEWSTEAD REVDAT 6 23-OCT-24 7BC7 1 REMARK REVDAT 5 11-AUG-21 7BC7 1 JRNL REVDAT 4 14-JUL-21 7BC7 1 JRNL REVDAT 3 07-JUL-21 7BC7 1 JRNL REVDAT 2 09-JUN-21 7BC7 1 JRNL REVDAT 1 12-MAY-21 7BC7 0 JRNL AUTH J.L.PARKER,J.C.DEME,G.KUTEYI,Z.WU,J.HUO,I.D.GOLDMAN, JRNL AUTH 2 R.J.OWENS,P.C.BIGGIN,S.M.LEA,S.NEWSTEAD JRNL TITL STRUCTURAL BASIS OF ANTIFOLATE RECOGNITION AND TRANSPORT BY JRNL TITL 2 PCFT. JRNL REF NATURE V. 595 130 2021 JRNL REFN ESSN 1476-4687 JRNL PMID 34040256 JRNL DOI 10.1038/S41586-021-03579-Z REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.300 REMARK 3 NUMBER OF PARTICLES : 341318 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7BC7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292113113. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : COMPLEX OF THE PROTON COUPLED REMARK 245 FOLATE TRANSPORTER AT PH 6.0 REMARK 245 BOUND TO PEMETREXED; PROTON- REMARK 245 COUPLED FOLATE TRANSPORTER; REMARK 245 NANOBODY REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5850.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 PRO A 4 REMARK 465 SER A 5 REMARK 465 ASP A 6 REMARK 465 PRO A 7 REMARK 465 PRO A 8 REMARK 465 THR A 9 REMARK 465 ALA A 10 REMARK 465 ALA A 11 REMARK 465 THR A 12 REMARK 465 PRO A 13 REMARK 465 PRO A 14 REMARK 465 ALA A 15 REMARK 465 PRO A 16 REMARK 465 PRO A 17 REMARK 465 PRO A 18 REMARK 465 PRO A 19 REMARK 465 ALA A 20 REMARK 465 ARG A 21 REMARK 465 ARG A 22 REMARK 465 CYS A 23 REMARK 465 LEU A 24 REMARK 465 PRO A 25 REMARK 465 LEU A 458 REMARK 465 GLN A 459 REMARK 465 TYR A 460 REMARK 465 SER A 461 REMARK 465 HIS A 462 REMARK 465 PHE A 463 REMARK 465 SER A 464 REMARK 465 ASP A 465 REMARK 465 ALA A 466 REMARK 465 SER A 467 REMARK 465 SER A 468 REMARK 465 SER A 469 REMARK 465 PRO A 470 REMARK 465 ALA A 471 REMARK 465 ASP A 472 REMARK 465 GLY A 473 REMARK 465 GLY A 474 REMARK 465 GLU A 475 REMARK 465 ASN A 476 REMARK 465 LEU A 477 REMARK 465 TYR A 478 REMARK 465 PHE A 479 REMARK 465 GLN A 480 REMARK 465 GLY B -2 REMARK 465 PRO B -1 REMARK 465 SER B 0 REMARK 465 GLN B 1 REMARK 465 SER B 119 REMARK 465 ALA B 120 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LYS A 249 OG1 THR A 252 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 28 -173.81 -175.65 REMARK 500 ASN A 65 37.51 -98.41 REMARK 500 ASP A 164 -163.24 -79.04 REMARK 500 TYR A 216 -13.34 77.53 REMARK 500 ILE A 217 -60.77 -125.36 REMARK 500 CYS A 237 18.55 -140.83 REMARK 500 LEU A 253 -9.30 78.53 REMARK 500 LYS A 261 45.56 -86.74 REMARK 500 LEU A 262 -35.07 -131.51 REMARK 500 LEU A 301 50.58 -93.60 REMARK 500 MET A 377 37.52 -94.76 REMARK 500 SER B 25 -179.95 -170.03 REMARK 500 PHE B 29 -10.25 70.69 REMARK 500 TRP B 47 128.14 -35.30 REMARK 500 ASP B 57 73.67 -100.51 REMARK 500 ALA B 92 -174.65 -171.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-12141 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE PROTON COUPLED FOLATE TRANSPORTER AT PH REMARK 900 6.0 BOUND TO PEMETREXED DBREF 7BC7 A 1 473 UNP E6Y8U5 E6Y8U5_CHICK 1 473 DBREF 7BC7 B -2 120 PDB 7BC7 7BC7 -2 120 SEQADV 7BC7 GLY A 474 UNP E6Y8U5 EXPRESSION TAG SEQADV 7BC7 GLU A 475 UNP E6Y8U5 EXPRESSION TAG SEQADV 7BC7 ASN A 476 UNP E6Y8U5 EXPRESSION TAG SEQADV 7BC7 LEU A 477 UNP E6Y8U5 EXPRESSION TAG SEQADV 7BC7 TYR A 478 UNP E6Y8U5 EXPRESSION TAG SEQADV 7BC7 PHE A 479 UNP E6Y8U5 EXPRESSION TAG SEQADV 7BC7 GLN A 480 UNP E6Y8U5 EXPRESSION TAG SEQRES 1 A 480 MET ALA ALA PRO SER ASP PRO PRO THR ALA ALA THR PRO SEQRES 2 A 480 PRO ALA PRO PRO PRO PRO ALA ARG ARG CYS LEU PRO ALA SEQRES 3 A 480 PRO SER VAL GLU PRO LEU LEU PHE LEU ALA THR LEU ALA SEQRES 4 A 480 LEU GLY LEU GLN VAL PRO LEU ALA THR GLN TYR LEU TRP SEQRES 5 A 480 ASP ARG LEU GLY ALA GLU ARG GLY TYR VAL GLY PRO ASN SEQRES 6 A 480 ALA SER SER PRO HIS GLY CYS GLY ASN GLY SER GLY ALA SEQRES 7 A 480 VAL ASP PRO LEU ARG GLU GLU VAL GLU ALA LEU VAL ALA SEQRES 8 A 480 HIS TRP ASN LEU CYS ILE ASN LEU GLY GLY PHE PHE VAL SEQRES 9 A 480 GLY LEU PHE SER VAL THR LEU PHE GLY PRO TRP SER ASP SEQRES 10 A 480 SER VAL GLY ARG ARG PRO VAL LEU VAL LEU PRO ALA VAL SEQRES 11 A 480 GLY MET ALA VAL GLN ALA ALA VAL TYR LEU LEU VAL MET SEQRES 12 A 480 TYR LEU ARG LEU HIS VAL ALA TYR LEU LEU LEU GLY ARG SEQRES 13 A 480 ILE ILE SER GLY LEU LEU GLY ASP TYR ASN LEU ILE LEU SEQRES 14 A 480 ALA GLY CYS PHE ALA SER VAL ALA ASP SER SER ASN GLN SEQRES 15 A 480 ARG THR ARG THR PHE ARG VAL ALA ILE LEU GLU ALA CYS SEQRES 16 A 480 LEU GLY VAL ALA GLY MET VAL ALA SER VAL GLY GLY GLY SEQRES 17 A 480 GLN TRP ARG LYS ALA GLU GLY TYR ILE ASN PRO PHE TRP SEQRES 18 A 480 LEU VAL LEU ALA ALA SER LEU ALA ALA ALA LEU TYR ALA SEQRES 19 A 480 ALA LEU CYS LEU GLN GLU THR VAL LYS GLN ARG ARG ALA SEQRES 20 A 480 ALA LYS LEU LEU THR LEU GLN HIS TYR LYS ALA VAL TYR SEQRES 21 A 480 LYS LEU TYR THR ALA PRO GLU ASP LEU SER SER ARG ARG SEQRES 22 A 480 LYS LEU ALA LEU TYR SER LEU ALA PHE PHE LEU LEU VAL SEQRES 23 A 480 THR VAL HIS PHE GLY THR LYS ASP LEU TYR VAL LEU TYR SEQRES 24 A 480 GLU LEU GLY SER PRO LEU CYS TRP ALA SER ASP LEU ILE SEQRES 25 A 480 GLY TYR GLY SER ALA ALA SER TYR LEU ALA TYR LEU SER SEQRES 26 A 480 SER LEU GLY GLY LEU ARG LEU LEU GLN LEU CYS LEU GLU SEQRES 27 A 480 ASP THR TRP VAL ALA GLU ILE GLY LEU ILE SER ASN ILE SEQRES 28 A 480 ALA GLY LEU VAL VAL ILE SER LEU ALA THR THR THR PRO SEQRES 29 A 480 LEU MET PHE THR GLY TYR GLY ILE MET PHE LEU SER MET SEQRES 30 A 480 ALA ALA THR PRO VAL ILE ARG ALA LYS LEU SER LYS LEU SEQRES 31 A 480 VAL SER GLU THR GLU GLN GLY ALA LEU PHE ALA SER VAL SEQRES 32 A 480 ALA CYS VAL GLU GLY LEU CYS SER LEU VAL ALA THR GLY SEQRES 33 A 480 VAL PHE ASN SER LEU TYR PRO SER THR LEU HIS PHE MET SEQRES 34 A 480 ARG GLY PHE PRO PHE LEU PHE GLY ALA ILE LEU LEU LEU SEQRES 35 A 480 ILE PRO ALA ALA ILE MET GLY TRP ILE GLU ILE GLN ASP SEQRES 36 A 480 SER ASN LEU GLN TYR SER HIS PHE SER ASP ALA SER SER SEQRES 37 A 480 SER PRO ALA ASP GLY GLY GLU ASN LEU TYR PHE GLN SEQRES 1 B 123 GLY PRO SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY SEQRES 2 B 123 LEU VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA SEQRES 3 B 123 ALA SER GLY PHE THR PHE SER ARG TYR TRP MET TYR TRP SEQRES 4 B 123 VAL ARG GLN ALA PRO GLY LYS GLY PRO GLU TRP LEU SER SEQRES 5 B 123 HIS MET ASN PRO SER GLY SER ASP ILE LYS TYR THR ASP SEQRES 6 B 123 SER VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA SEQRES 7 B 123 LYS ASN THR LEU TYR LEU GLN MET ASN SER LEU LYS PRO SEQRES 8 B 123 ASP ASP THR ALA VAL TYR TYR CYS VAL ALA ASP ARG ARG SEQRES 9 B 123 ALA LEU GLY SER PRO GLU TYR TRP GLY GLN GLY THR GLN SEQRES 10 B 123 VAL THR VAL SER SER ALA HET LYA A 501 31 HETNAM LYA 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3- HETNAM 2 LYA D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC HETNAM 3 LYA ACID HETSYN LYA LY231514 FORMUL 3 LYA C20 H21 N5 O6 HELIX 1 AA1 VAL A 29 ARG A 59 1 31 HELIX 2 AA2 ASP A 80 GLY A 120 1 41 HELIX 3 AA3 GLY A 120 ARG A 146 1 27 HELIX 4 AA4 ALA A 150 LEU A 162 1 13 HELIX 5 AA5 ASP A 164 ASP A 178 1 15 HELIX 6 AA6 THR A 184 ARG A 211 1 28 HELIX 7 AA7 ASN A 218 CYS A 237 1 20 HELIX 8 AA8 TYR A 256 THR A 264 1 9 HELIX 9 AA9 SER A 270 GLU A 300 1 31 HELIX 10 AB1 ALA A 308 GLN A 334 1 27 HELIX 11 AB2 GLU A 338 LEU A 359 1 22 HELIX 12 AB3 THR A 362 MET A 373 1 12 HELIX 13 AB4 LEU A 375 MET A 377 5 3 HELIX 14 AB5 ALA A 378 VAL A 391 1 14 HELIX 15 AB6 GLU A 395 THR A 425 1 31 HELIX 16 AB7 GLY A 431 LEU A 441 1 11 HELIX 17 AB8 LEU A 441 SER A 456 1 16 HELIX 18 AB9 LYS B 87 THR B 91 5 5 SHEET 1 AA1 4 GLN B 3 GLU B 6 0 SHEET 2 AA1 4 LEU B 18 SER B 25 -1 O ALA B 23 N VAL B 5 SHEET 3 AA1 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA1 4 PHE B 68 ASP B 73 -1 N SER B 71 O TYR B 80 SHEET 1 AA2 3 SER B 49 MET B 51 0 SHEET 2 AA2 3 TRP B 33 ARG B 38 -1 N MET B 34 O MET B 51 SHEET 3 AA2 3 ALA B 98 ASP B 99 -1 O ASP B 99 N TRP B 33 SHEET 1 AA3 4 SER B 49 MET B 51 0 SHEET 2 AA3 4 TRP B 33 ARG B 38 -1 N MET B 34 O MET B 51 SHEET 3 AA3 4 ALA B 92 TYR B 95 -1 O TYR B 95 N VAL B 37 SHEET 4 AA3 4 THR B 113 VAL B 115 -1 O VAL B 115 N ALA B 92 SSBOND 1 CYS A 72 CYS A 306 1555 1555 2.03 SSBOND 2 CYS B 22 CYS B 96 1555 1555 2.04 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000